3OOD

Structure of OpdA Y257F mutant soaked with diethyl 4-methoxyphenyl phosphate for 20 hours.

3OOD の概要

• エントリーDOI: 10.2210/pdb3ood/pdb
• 分子名称: Phosphotriesterase, COBALT (II) ION, DIETHYL 4-METHOXYPHENYL PHOSPHATE, ... (4 entities in total)
• 機能のキーワード: binuclear metallohydrolase, organophosphate hydrolysis, diethyl 4-methoxyphenyl phosphate, bioremediation, tim barrel, phosphotriesterase, binuclear metal ion binding, hydrolase
• 由来する生物種: Agrobacterium tumefaciens (Agrobacterium tumefaciens)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 36051.72

構造登録者

Ely, F.,Guddat, L.W.,Ollis, D.L.,Schenk, G. (登録日: 2010-08-31, 公開日: 2011-11-02, 最終更新日: 2023-12-06)

主引用文献

Ely, F.,Hadler, K.S.,Gahan, L.R.,Guddat, L.W.,Ollis, D.L.,Schenk, G.
The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis.
Biochem.J., 432:565-573, 2010

PubMed Abstract: The OP (organophosphate)-degrading enzyme from Agrobacterium radiobacter (OpdA) is a binuclear metallohydrolase able to degrade highly toxic OP pesticides and nerve agents into less or non-toxic compounds. In the present study, the effect of metal ion substitutions and site-directed mutations on the catalytic properties of OpdA are investigated. The study shows the importance of both the metal ion composition and a hydrogen-bond network that connects the metal ion centre with the substrate-binding pocket using residues Arg254 and Tyr257 in the mechanism and substrate specificity of this enzyme. For the Co(II) derivative of OpdA two protonation equilibria (pKa1 ~5; pKa2 ~10) have been identified as relevant for catalysis, and a terminal hydroxide acts as the likely hydrolysis-initiating nucleophile. In contrast, the Zn(II) and Cd(II) derivatives only have one relevant protonation equilibrium (pKa ~4-5), and the μOH is the proposed nucleophile. The observed mechanistic flexibility may reconcile contrasting reaction models that have been published previously and may be beneficial for the rapid adaptation of OP-degrading enzymes to changing environmental pressures.

PubMed: 20868365
DOI: 10.1042/BJ20101054

実験手法

X-RAY DIFFRACTION (1.89 Å)